The Council on American-Islamic Relations (CAIR) refused for many years to condemn terrorist groups that seek to destroy Israel. The organization has never addressed its past affiliations with the Islamic Association for Palestine (IAP), which has been described by the U.S. government as part of "Hamas' propaganda apparatus."

On the fifth anniversary of the Madrid bombings in March 2009, CAIR condemned acts of terrorism bygroups designated by the U.S. Department of State as a Foreign Terrorist Organization, acknowledging that Hamas is on that list. The statement, however, did not represent a genuine break from CAIR's past because it did not address its own historical links to Hamas.

CAIR's statement also came after the Holy Land Foundation (HLF) trial, during which information on CAIR's links to Hamas was produced, and after the FBI limited its contact with CAIR. John Miller, an FBI spokesman has said that "the FBI has had to limit its formal contact with CAIR field offices until certain issues are addressed by CAIR's national headquarters."

Furthermore, while CAIR's statement acknowledged the fact that Hamas is on the list of terror organizations, it avoided making any independent judgment of Hamas, its ideology or goals.

Over the years, CAIR representatives have argued that Hezbollah and Palestinian terror organizations are patently different from Al Qaeda—which CAIR has denounced—and thus cannot be viewed as a similar threat. Yet, the group has participated in and endorsed many rallies where support for terrorist organizations was undeniable, failing to distance itself from such public expressions.

CAIR has often dismissed terror-related trials in the U.S. such as the Sami al-Arian and HLF cases, portraying the defendants as legitimate advocates for Palestinians and as victims of Israeli political influence in the U.S.

CAIR's position on terrorism is further complicated by its ambiguous stance on innocent civilians - a notion that allows for an interpretation that all Israelis are a legitimate target because of Israel's mandatory military service. This position was supported by Ghazi Kankan, the former executive director of CAIR's New Yorkchapter, who said that he considers all Israelis over the age of 18 to be "military" because "they are all reserves." CAIR leaders have also expressed support for Sheik Yusuf Qaradawi, the most prominent Muslim cleric to sanction attacks on Israeli civilians based on this rational.

The following examples further demonstrate CAIR's positions on terrorism:

December 2008 – January 2009: CAIR organized several anti-Israel rallies in response to Israel's military action against Hamas in Gaza. At one rally in Washington D.C. on January 10, protestors marched with signs that read: "Jewish Run Media Hides Jewish Terrorism" and "Jewish Controlled Congress Supports Jewish Terrorism."

August 12, 2006: CAIR helped to coordinate a number of demonstrations in support of Hezbollah and "resistance" groups fighting American forces in Iraq. Speakers and protesters at the demonstrations hailed Hezbollah and Hamas and denounced Israel's existence. Protesters also equated Zionism with Nazism and called for Hezbollah to bomb Israeli cities.

July 7, 2004: Ibrahim Hooper, CAIR's spokesman, defended Sheik Yusuf Qaradawi, a Qatar-based Muslim cleric known for promoting violence against Jews and Israelis, in an interview with BBC. Hooper described Qaradawi as "respectable," adding: "I don't think there's any incitement of violence on his part."

Fall 2003: Nihad Awad, CAIR's national executive director, publicly endorsed the Islamic American University (IAU), a Michigan-based subsidiary of the Muslim American Society (MAS). IAU's chairman is Sheikh Yusuf Qaradawi. Awad commended the IAU for its "ability to educate American Muslims and future generations on how to effectively introduce Islam as a civilized way of life and perhaps as an alternative to the mainstream."

April 20, 2002: Nihad Awad addressed an anti-Israel rally organized by the ANSWER Coalition in Washington D.C. while standing next to an oversized Hezbollah flag. Other speakers at the rally called for Israel to be dismantled, and protesters held signs comparing Zionism and Israel to Nazi Germany while chanting violent and anti-Semitic slogans.

October 12, 2001: Ghazi Kankan, executive director of CAIR's New York office at the time, defended Hamas's targeting of Israeli civilians. He told the Jewish Week that, like Hamas, he considered all Israelis over the age of 18 to be "military" because "they are all reserves."

April 19, 1996: In its first published report on anti-Muslim discrimination, titled "The Price of Ignorance," CAIR cited the arrest of Sheik Omar Abdel Rahman, the Egyptian cleric serving a life sentence for conspiracy to blow up New York landmarks in 1993, and the detention of senior Hamas leader Musa Abu Marzuq, as "incidents of bias and violence" against Muslims in the U.S.

March 22, 1994: During a panel discussion at Barry University in Florida, Nihad Awad said: "I used to support the PLO, and I used to be the President of the General Union of Palestine Students which is part of the PLO here in the United States, but after I researched the situation inside Palestine and outside, I am in support of the Hamas movement more than the PLO."